9KGA | pdb_00009kga

Crystal structure of SpTx1 toxin

• PDB DOI: https://doi.org/10.2210/pdb9KGA/pdb

• Classification: TOXIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2025-11-12 
• Deposition Author(s): Chen, L., Wang, M., Fan, C.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Structure of SpTx1 at 1.9 Angstroms resolution

Chen, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.17 kDa 
• Atom Count: 3,000 
• Modeled Residue Count: 329 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SpTx1	A, B, C, D, E, F	56	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.485	α = 90
b = 60.485	β = 90
c = 169.854	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Chen, L., Wang, M., Fan, C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFA1303000
National Natural Science Foundation of China (NSFC)	China	32225027

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release